Variant report

Variant	rs12309413
Chromosome Location	chr12:57513879-57513880
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57502941..57507087-chr12:57511781..57514626,3	K562	blood:
2	chr12:57503627..57505712-chr12:57512717..57514306,2	K562	blood:
3	chr12:57398143..57400588-chr12:57512007..57514365,2	MCF-7	breast:
4	chr12:57513705..57517929-chr12:57519571..57523661,4	K562	blood:

Variant related genes	Relation type
ENSG00000166860	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000123384	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10467124	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876963	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172106	0.86[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172110	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172111	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12298170	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12312693	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322902	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12368672	0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs3001425	0.85[ASN][1000 genomes]
rs3001426	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs324012	0.83[EUR][1000 genomes]
rs324014	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4759275	1.00[CEU][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4759276	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57505800-57521800	Weak transcription	Spleen	Spleen
2	chr12:57506200-57520000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:57506200-57520400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:57506600-57520400	Weak transcription	Stomach Mucosa	stomach
5	chr12:57506600-57520600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:57506600-57520600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:57506800-57518200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:57506800-57519200	Weak transcription	Liver	Liver
9	chr12:57512800-57520200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:57512800-57520400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:57513000-57514400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:57513000-57520400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:57513400-57520600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:57513600-57518000	Weak transcription	NHLF	lung
15	chr12:57513600-57518200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:57513600-57520400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:57513600-57520800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:57513800-57518000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:57513800-57520400	Weak transcription	NHDF-Ad	bronchial
20	chr12:57513800-57520600	Weak transcription	Osteobl	bone

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